Abstract P2-01-04: A method for comprehensive genomic analysis of cell free DNA
Authors: S Parpart-Li, SV Angiuoli, B Chesnick, K Galens, S Jones, M Kadan, L Kann, K Lytle, D Murphy, M Nesselbush, J Phallen, D Riley, M Shukla, T Zhang, H Husain, V Velculescu, LA Diaz, M Sausen
Journal: Cancer Research (2016)

Abstract Circulating tumor DNA (ctDNA) is released from tumor tissue into the blood, carries tumor specific genetic alterations, and can be analyzed through noninvasive "liquid biopsy" approaches to identify genetic alterations in cancer patients. Liquid biopsies offer a considerable advantage as they may eliminate the need for invasive tissue biopsies and allow for the detection of alterations in multiple metastatic lesions throughout the course of therapy. However, the fraction of ctDNA obtained from a blood sample is often very low (&amp;lt;1.0%) and can be difficult to detect. Additionally, most methods to evaluate circulating tumor DNA (ctDNA) interrogate single hot spot mutations or few genetic alterations. The next generation of ctDNA assays must interrogate multiple gene regions from a single sample with high precision and accuracy and need to evaluate all forms of actionable genomic alterations including point mutations, amplifications, and translocations. To address these issues, we have developed a ctDNA approach called PlasmaSelect to detect somatic sequence mutations, amplifications and translocations at low allele frequencies in the circulation of cancer patients. Utilizing digital genomic approaches, PlasmaSelect achieves high sensitivity and specificity while interrogating &amp;gt;250,000 nucleotides spanning 63 well-established cancer genes. In addition to sequence mutations in the entire coding region of 18 genes and the exons of 40 genes that are frequently mutated in cancer, PlasmaSelect also performs a comprehensive genomic analysis of amplifications in 57 genes and translocations in 10 genes significant in cancer tumorigenesis. To evaluate the PlasmaSelect approach, we performed dilution series using tumor-derived DNA, containing well-characterized somatic mutations, in the presence of wild-type DNA. PlasmaSelect was able to detect genetic alterations with high specificity and a lower level of detection of 0.10% for sequence mutations and translocations, as well as a focal amplification of ERBB2 with a lower level of detection of 0.20%. We evaluated the clinical utility of PlasmaSelect for detection of genetic alterations in the plasma and matched tissue biopsy specimens from late stage cancer patients. These analyses demonstrated high concordance between the somatic sequence mutations, amplifications, and translocations identified in the tumor sample and those identified directly in the plasma, including alterations in both driver genes as well as those related to acquired resistance to targeted therapies. PlasmaSelect provides a non-invasive platform to enable liquid biopsy detection of clinically relevant genetic alterations across a large number of genomic loci. Citation Format: Parpart-Li S, Angiuoli SV, Chesnick B, Galens K, Jones S, Kadan M, Kann L, Lytle K, Murphy D, Nesselbush M, Phallen J, Riley D, Shukla M, Zhang T, Husain H, Velculescu V, Diaz, Jr LA, Sausen M. A method for comprehensive genomic analysis of cell free DNA. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-01-04.